note
brap
<p>Hey anonymous,</p>
<p>I could be way off base here, but it almost sounds like you want an array of counters, where each element of the array represents the position of the line you're counting. Something along the order of (untested):</p>
<code>
if ($split_seq_to_examine[$j] eq 'A') {$count_A[$j]++;}
elsif ($split_seq_to_examine[$j] eq 'T') {$count_T[$j]++;}
elsif ($split_seq_to_examine[$j] eq 'C') {$count_C[$j]++;}
elsif ($split_seq_to_examine[$j] eq 'G') {$count_G[$j]++;}
elsif ($split_seq_to_examine[$j] eq '-') {$count_non[$j]++;}
</code>
<p>To find out what you have in, say, position 56, look at <c>$count_A[56], $count_T[56], $count_G[56], and $count_C[56]</c>.</p>
1007821
1007821